Underwater Cave Bones Could Solve an Extinct Megafauna Mystery
Deep beneath the pastures of South Australia’s Limestone Coast, flooded cave systems have quietly preserved animal bones for centuries, in some cases thousands of years. Scientists have long known that these underwater graveyards hold extraordinary fossil records. What they lacked, until now, was a reliable way to read them.
A New Way to Read Old Bones
Researchers led by Griffith University have developed the first framework for interpreting how the remains of extinct megafauna and other animals accumulated, survived, and changed after entering underwater caves. The study, led by PhD candidate Meg Walker under the supervision of Australian Research Centre for Human Evolution director Professor Julien Louys, was published in the journal PLOS One.
“By analysing animal bones from two underwater cave systems in South Australia, we have revealed how different cave environments leave distinct preservation fingerprints on skeletal remains,” Walker said. “Backed by radiocarbon-dated bones, we tracked how skeletons accumulated and were modified over decades and centuries in underwater caves, then compared them to those buried in dry caves.”
Diving Into Green Waterhole and Gouldens Sinkhole
Walker and her team, working with specialist divers from the Cave Divers Association of Australia, collected historical animal bones from two underwater cave systems near Mount Gambier, South Australia, known as Green Waterhole and Gouldens Sinkhole. The recovered remains came from both native and introduced species, including kangaroos, emus, dingoes, possums, quolls, and swamp rats alongside cows, sheep, and pigs. Some specimens may date back to the first European settlement of the area in the 1840s.
Because these more recent bones came from known, relatively well-understood animals and time periods, they gave researchers a way to test how underwater and dry caves treat skeletal remains differently, before applying those lessons to far older, more mysterious fossil deposits from extinct megafauna.
What the Bones Revealed
Using techniques ranging from broad spatial analysis down to elemental composition and proteins preserved in ancient cells, the team found that underwater caves often preserve bones remarkably well, keeping their structure and surface detail intact. At the same time, submerged environments left behind their own unmistakable chemical and biological traces, shaped largely by how much light reached a given part of the cave.
Near sunlit cave entrances, algae and other aquatic plants colonized bone surfaces, leaving behind recognizable growth signatures. Deeper in the cave systems, in zones where sunlight never penetrates, no plants could grow, and bones in these areas often stayed close to pristine. Bones recovered from dry caves told a different story altogether. Lacking any aquatic markings, they instead showed damage from land-based bacteria and long grooves carved by plant roots searching for moisture and nutrients.
Why This Matters for Australia’s Vanished Giants
Australia was once home to an extraordinary array of Ice Age megafauna, including the giant wombat relative Diprotodon, the predatory marsupial lion Thylacoleo, and outsized short-faced kangaroos. Exactly why these animals went extinct toward the end of the Pleistocene remains one of the most debated questions in Australian and global palaeontology, with researchers still weighing the relative roles of human arrival and environmental change.
Answering that question depends partly on reconstructing the environments these animals actually lived in, information that is often locked inside the caves where their remains eventually settled. Until now, researchers had limited ability to tell whether a fossil’s condition reflected the environment it lived in, the way it died, or simply what happened to its bones after they were submerged or buried, sometimes for tens of thousands of years.
“This study has delivered the first framework for interpreting how megafauna fossils formed, survived, and changed in underwater caves,” Walker said. “It will provide archaeologists and palaeontologists worldwide with a powerful new tool for reconstructing past environments and histories in these challenging conditions.”
Fragile Time Capsules Worth Protecting
The Mount Gambier region contains hundreds of similar limestone cave systems, many of which likely hold comparable fossil deposits still waiting to be studied. Researchers involved in the broader project have previously called for stronger protections for these sites, both to preserve their scientific value and to reduce risks to divers exploring them without adequate training.
With this new preservation framework in hand, scientists now have a clearer way to distinguish genuine ecological signals from the noise introduced by a bone’s long journey through darkness, water, and time, bringing them a step closer to understanding what finally drove some of Australia’s largest Ice Age animals to extinction.
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